Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils DOI Creative Commons
Zhi-Bo Zhao, Ji‐Zheng He, Stefan Geisen

et al.

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 27, 2019

Agricultural food production is at the base of and fodder, with fertilization having fundamentally continuously increased crop yield over last decades. The performance crops intimately tied to their microbiome as they together form holobionts. importance for plant is, however, notoriously ignored in agricultural systems disconnects dependency plants often plant-beneficial microbial processes. Moreover, we lack a holistic understanding how regimes affect soil microbiome. Here, examined effect 2-year regime (no nitrogen control, fertilization, plus straw amendment) on entire microbiomes (bacteria, fungi, protist) three common types cropped maize two seasons.We found that application fertilizers more strongly affected protist than bacterial fungal communities. Nitrogen indirectly reduced diversity through changing abiotic properties communities which differed between sampling seasons. fertilizer amendment had greater effects physicochemical addition alone. even straw, network complexity, suggesting tightened interactions.Together, our results suggest protists are most susceptible component fertilizers. As also exhibit strongest seasonal dynamics, serve sensitive bioindicators changes. Changes might have long-term if some key hubs govern complexities top predators altered. This study serves stepping stone promote promising agents targeted engineering help reducing exogenous unsustainably high pesticide applications.

Language: Английский

A few Ascomycota taxa dominate soil fungal communities worldwide DOI Creative Commons
Eleonora Egidi, Manuel Delgado‐Baquerizo, Jonathan M. Plett

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: May 30, 2019

Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across globe. Our findings indicate that 83 phylotypes (<0.1% of retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate globally. We identify patterns drivers fungal taxa occurrence, present a map distribution worldwide. Whole-genome comparisons with less dominant, point significantly higher number genes related stress-tolerance resource uptake fungi, suggesting they might be better colonising wide range environments. constitute major advance our understanding ecology have implications for development strategies preserve them ecosystem provide.

Language: Английский

Citations

542
Erosion reduces soil microbial diversity, network complexity and multifunctionality DOI Creative Commons
Liping Qiu, Qian Zhang,

Hansong Zhu

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2474 - 2489

Published: March 12, 2021

Abstract While soil erosion drives land degradation, the impact of on microbial communities and multiple functions remains unclear. This hinders our ability to assess true ecosystem services restore eroded environments. Here we examined effect at two sites with contrasting texture climates. Eroded plots had lower network complexity, fewer taxa, associations among relative non-eroded plots. Soil also shifted community composition, decreased abundances dominant phyla such as Proteobacteria, Bacteroidetes, Gemmatimonadetes. In contrast, led an increase in some bacterial families involved N cycling, Acetobacteraceae Beijerinckiaceae. Changes microbiota characteristics were strongly related erosion-induced changes multifunctionality. Together, these results demonstrate that has a significant negative diversity functionality.

Language: Английский

Citations

523
Effects of plastic mulch film residues on wheat rhizosphere and soil properties DOI Creative Commons
Yueling Qi, Adam Ossowicki, Xiaomei Yang

et al.

Journal of Hazardous Materials, Journal Year: 2019, Volume and Issue: 387, P. 121711 - 121711

Published: Nov. 17, 2019

Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results serious environmental concern for agroecosystems. As an alternative, biodegradable films stand promising products to minimize debris accumulation and reduce soil pollution. However, the effects from traditional on soil-plant system are not well studied. In this study, we used controlled pot experiment investigate macro- micro- sized low-density polyethylene mulch rhizosphere bacterial communities, volatile profiles chemical properties. Interestingly, identified significant communities blend volatiles emitted rhizosphere. For example, treatments with plastics, bacteria genera like Bacillus Variovorax were present higher relative abundances compounds dodecanal exclusively produced treatment microplastics. Furthermore, differences pH, electrical conductivity C:N ratio observed across treatments. Our study provides evidence both biotic abiotic impacts system, suggesting urgent need more research examining their

Language: Английский

Citations

504
Host selection shapes crop microbiome assembly and network complexity DOI Creative Commons
Chao Xiong, Yong‐Guan Zhu, Juntao Wang

et al.

New Phytologist, Journal Year: 2020, Volume and Issue: 229(2), P. 1091 - 1104

Published: Aug. 27, 2020

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere bulk soil) multiple compartment niches (rhizoplane, root endosphere, phylloplane, leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate along soil-plant continuum is shaped predominantly by niche species rather than site or practice. From epiphytes endophytes, selection pressure sequentially increased diversity network complexity consequently reduced, with strongest effect endosphere. Source tracking indicates mainly derived gradually enriched filtered plant niches. Moreover, were dominated a few dominant taxa (c. 0.5% of phylotypes), bacilli identified as important biomarker for wheat barley Methylobacteriaceae maize. work provides comprehensive empirical evidence on selection, potential sources enrichment assembly, has implications future management manipulation sustainable agriculture.

Language: Английский

Citations

498
From hairballs to hypotheses–biological insights from microbial networks DOI Creative Commons

Lisa Röttjers,

Karoline Faust

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 761 - 780

Published: July 25, 2018

Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.

Language: Английский

Citations

476
Microplastics from mulching film is a distinct habitat for bacteria in farmland soil DOI
Mengjun Zhang,

Yanran Zhao,

Xiao Qin

et al.

The Science of The Total Environment, Journal Year: 2019, Volume and Issue: 688, P. 470 - 478

Published: June 8, 2019

Language: Английский

Citations

463
The structure and function of the global citrus rhizosphere microbiome DOI Creative Commons
Jin Xu, Yunzeng Zhang, Pengfan Zhang

et al.

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 14, 2018

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax Paraburkholderia, some which are potential plant beneficial microbes. also identify over-represented microbial traits mediating plant-microbe microbe-microbe interactions, nutrition acquisition promotion rhizosphere. results provide valuable information guide isolation culturing and, potentially, harness power improve production

Language: Английский

Citations

424
Innovations to culturing the uncultured microbial majority DOI
William H. Lewis,

Guillaume Tahon,

Patricia Geesink

et al.

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 19(4), P. 225 - 240

Published: Oct. 22, 2020

Language: Английский

Citations

404
The proportion of soil-borne pathogens increases with warming at the global scale DOI
Manuel Delgado‐Baquerizo, Carlos A. Guerra, Concha Cano‐Díaz

et al.

Nature Climate Change, Journal Year: 2020, Volume and Issue: 10(6), P. 550 - 554

Published: May 11, 2020

Language: Английский

Citations

400
Linking bacterial community composition to soil salinity along environmental gradients DOI Creative Commons
Kristin Rath, Noah Fierer, Daniel V. Murphy

et al.

The ISME Journal, Journal Year: 2018, Volume and Issue: 13(3), P. 836 - 846

Published: Nov. 16, 2018

Abstract Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on microbial communities fact that it can be difficult disentangle from those other variables may co-vary with salinity. Here we use trait-based approach identify direct bacterial across two gradients. Through dose–response relationships between and growth, quantified distributions trait salt tolerance within communities. Community was closely correlated salinity, indicating strong filtering effect Accompanying increases were consistent shifts community composition. We identified specific taxa increased relative abundances tolerance, which could used bioindicators for high tolerance. also observed pH gradients, pH. propose phenotypic aggregated at level useful study role environmental factors filters

Language: Английский

Citations

396